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If you're working on a 1040:
I am working on a Form 1065. But I followed the guidance you provided for 1040 prep as the screens seem similar for the Form 1065. The amended return box was not checked but the pdf of the return is printing with the Amended Return box checked on page 1 and also on each K-1. To me, it seems there is a problem with the software as nothing in my input should cause it to print as an amended return.
Thank you for your response.
I had the same X-checkmarked Amended Return box on a Form 1120S and could not remove it. I discovered that in the Profile tab for the return, the Federal Amended box was checked in the Select for E-File column was wrongly checked. Unchecking it removed the X for Amended Return. Fixed.